Re: MMPBSA Energy Calculations using VMD (Post-Processing)

From: Jason Swails (
Date: Mon Apr 14 2014 - 13:02:08 CDT

On Mon, 2014-04-14 at 13:24 -0400, Kenno Vanommeslaeghe wrote:
> I'm not sure the PBSA radii for AMBER atom types are accurate when used
> with CHARMM charges.
> Also, as a reminder, if you use the CHARMM FF for your ligand, you have to
> use the CHARMM FF for your protein as well.
> Finally, I'd like to point out the "as long as the particle density
> reaches approximately bulk outside of the cutoff" assumption is not always
> valid. It may not matter for implicit solvent, but I just wanted to have
> this on the record so that people who work on other things don't get the
> wrong idea. For instance, membranes in explicit solvent are crazy
> sensitive to small details in the nonbonded interactions at long range.

Well sure, but then the assumption of an "isotropic distribution of
particles beyond the cutoff" breaks down as membrane systems are
decidedly NOT isotropic.

For membrane simulations (or surface simulations or simulations with any
anisotropic particle distribution) I defer to the relevant literature.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher

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